DNA forms nano waffles

By
Kimberly Patch,
Technology Research NewsResearchers are working to control the
way DNA strands interact with each other in order to coax the molecules
to form tiny structures. Such structures could eventually serve as microscopic
machines and as templates capable of causing other materials and devices
to automatically assemble molecule-by-molecule.

Researchers from Duke University have moved DNA construction methods
a step forward by coaxing DNA strands to lock together into tiles made
up of nine single strands of DNA that can further self-assemble into lattices.
The ribbon- and sheet-shaped lattices can be used as devices or as templates
to construct devices from other materials.

The researchers demonstrated one set of tiles that self-assembled
into a tiny protein detector, and another set that assembled into ribbons
that served as templates for precisely formed silver nanowires.

DNA is made up of four bases -- adenine, cytosine, guanine and
thymine -- attached to a sugar-phosphate backbone. Strands of DNA connect
to each other when strings of bases pair up -- adenine with thymine, and
cytosine with guanine.

The tiles form when single-stranded DNA molecules self-assemble
into a branched structure, said Hao Yan, an assistant research professor
of computer science at Duke University. "We make the DNA strands arrange
themselves into cross-shaped tiles capable of forming molecular bonds
on all four ends of the cross arms," said Yan.

The researchers were able to make the tiles connect to each other
to form a square, waffle-patterned grid or a waffle-patterned long ribbon
by making tiles with different "sticky end" configurations. Sticky ends
are portions of DNA strands that remain unconnected when the nine DNA
strands connect together to form the tile and can later connect to matching
DNA segments. "DNA tiles can carry sticky ends that preferentially match
the sticky ends of another particular DNA tile," said Yan.

The tiles were originally designed to form perfectly flat lattices,
but when the researchers reprogrammed the tiles by changing the sticky
ends so that the tile faces would all orient in the same direction up
or down, the tiles curved slightly in opposite directions to form a long,
narrow ribbon whose surfaces were waffled, said Yan. A second modification
that caused each tile face to point in the opposite direction from its
neighbor resulted in the wider grid structure.

The method is particularly useful because "we can easily achieve
two types of lattice by slightly changing the sticky-ends without changing
the tile structure itself," said Yan.

DNA makes a useful template because many other materials can chemically
attach to DNA. "Self-assembled DNA arrays provide excellent templates
for spatially positioning other molecules with... precision," said Yan.

The researchers formed a device that detects the protein streptavidin
by adding the molecule biotin to one of the DNA strands in each grid tile.
Streptavidin connects to biotin.

The researchers made precisely-formed silver nanowire using the
ribbon structure, said Yan. "We used a two-step chemical procedure to
coat silver onto the DNA nanoribbons to produce electricity-conducting
nanowires," he said.

Such wire can eventually be used to interconnect nanoscale devices
with micron-scale devices, said Yan. Connecting relatively large microscopic
objects, like those around the size of a cell, to relatively small ones,
like those around the size of a molecule, is a major challenge simply
because the size difference is so vast. A red blood cell, for instance,
is, at 5 microns across, about 15 times narrower than a human hair, but
50,000 times larger than a hydrogen atom.

The method could eventually be used to construct many types of
materials and devices, including electronics, molecule-by-molecule. Such
precise control over construction promises to enable materials that have
new properties, and electronics that are very efficient.

The researchers are working on designing more complicated DNA
nanostructures and working out chemical methods to attach nanoelectronic
components like carbon nanotubes to DNA, he said.

The ultimate goal is to use DNA as a scaffold to organize any
useful material into nano-size devices, sensors and even factories, said
Yan.

The technology could be ready for practical applications within
five years, said Yan.

Yan's research colleagues were Sung Ha Park, Gleb Finkelstein,
John H. Reif and Thomas H. LaBean. The work appeared in the September
26, 2003 issue of Science. The research was funded by the National
Science Foundation (NSF) and the Defense Advanced Research Projects Agency
(DARPA).